On my desktop (Xubuntu 16.04) they both open a new window. Changing the option "Open new terminals in Tab/Window" under "Edit > Preferences > General" does not affect the behavior (on the desktop). I want to open tabs, what to do?

Yes I know but I have it as a makefile command that opens all my stuff. Thanks anyway:)
– Jonatan ÖströmMay 24 at 14:46

Is there a specific reason you're not using Xubuntu's default terminal?
– DK BoseMay 24 at 15:51

And could you edit your question to post the output of ls -l ~/.config/dconf/user?
– DK BoseMay 24 at 16:01

Looks like a bug to me, file a bug report. If you set Open new terminals in Tab in Preferences you should be able to open a new tab in the current window by choosing Files > Open Terminal. Remind that different versions of gnome-terminal are installed in your systems.
– mook765May 24 at 17:07